1ISV,1V6W,1KNL,1KNM,1MC9,3A22,1XYF,2D1Z,3A21,3A23,5GQD


Conserved Protein Domain Family
beta-trefoil_Ricin_XLN-like

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cd23418: beta-trefoil_Ricin_XLN-like 
ricin B-type lectin domain, beta-trefoil fold, found in Streptomyces olivaceoviridis endo-1,4-beta-xylanase and similar proteins
The family includes Streptomyces olivaceoviridis endo-1,4-beta-xylanase (XLN, EC 3.2.1.8), Streptomyces avermitilis beta-L-arabinopyranosidase (EC 3.2.1.185), and Streptomyces coelicolor extracellular exo-alpha-L-arabinofuranosidase (ABF, EC 3.2.1.55). XLN, also called xylanase, or 1,4-beta-D-xylan xylanohydrolase, belongs to the glycosyl hydrolase 10 (cellulase F) family. It contributes to hydrolyze hemicellulose, the major component of plant cell walls. XLN contains a (beta/alpha)8-barrel as a catalytic domain, a family 13 carbohydrate binding module (CBM13) as a xylan binding domain (XBD) and a Gly/Pro-rich linker between them. Beta-L-arabinopyranosidase belongs to the glycosyl hydrolase 27 (GH27) family. It has a GH27 catalytic domain, an antiparallel beta-domain containing Greek key motifs, another antiparallel beta-domain forming a jellyroll structure, and a CBM13 module. ScAraf62A, also called ABF, or arabinosidase, or arabinoxylan arabinofuranohydrolase, belongs to the glycosyl hydrolase 62 (GH62) family. It is involved in the degradation of xylan and is a key enzyme in the complete degradation of the plant cell wall. It has a specific arabinofuranose-debranching activity on xylan from gramineae. It acts synergistically with xylanases and binds specifically to xylan. ScAraf62A comprises a CBM13 module at its N-terminus and a catalytic domain at its C-terminus. This model corresponds to the CBM13 module, which is a ricin B-type lectin domain with a beta-trefoil fold, characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding pocket.
Statistics
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PSSM-Id: 467297
Aligned: 31 rows
Threshold Bit Score: 117.836
Created: 16-Mar-2021
Updated: 27-Apr-2023
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:sugar binding site [chemical binding site]
Evidence:
  • Comment:sugar binding pocket within alpha subdomain
  • Structure:1V6W; Streptomyces Olivaceoviridis endo-1,4-beta-d-xylanase in complex with 2(2)-4-O-methyl-alpha-D-glucuronosyl-xylobiose, contacts at 4A
  • Structure:3A22; Streptomyces avermitilis beta-L-arabinopyranosidase in complex with L-arabinose, contacts at 4A
  • Structure:1ISV; Streptomyces Olivaceoviridis xylanase in complex with xylose, contacts at 4A
  • Structure:1KNM; Streptomyces Lividans endo-1,4-beta-xylanase A in complex with lactose, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                          ####             # #  #   ##                                  
1ISV_A       308 PPSGGGQIKGv-gSGRCLDVPNAst----tdGTQVQLYDCHSAtNQQWTYTd--aGELRVYg---DKCLDAAGtgn---- 373 Streptomyces ol...
1V6W_A       308 PPSGGGQIKGv-gSGRCLDVPNAst----tdGTQVQLYDCHSAtNQQWTYTd--aGELRVYg---DKCLDAAGtgn---- 373 Streptomyces ol...
ESQ80570      24 SYAGTQVIASgtaVGKCLDVAGN--------TGAIVLWGCHGGsNQNFVFAsgnyGQLKVN----DKCLSTSAvsfnq-- 89  Asticcacaulis s...
WP_023454480 171 EITGTPSIASyyvQGLCLEAKGA--------KGEISIEVCDRSaGQDFRFKsgnsGAIIQG----DKCLTTTGqg----- 233 Asticcacaulis s...
TAD82098      25 SISGMPVIASyhaQGRCLDMRAS--------DRQLLLWKCHGGsNQIFRFVsgnyGMISLGd---QRCLTIGAss----- 88  Sphingomonadale...
ALP39433      55 REEKGGQLLAs--SGKCLDIAGGir-----nGNRLQLWDCHGGdNQRFRLDg---DRVRIG----DKCLDVSGndrd--- 117 Aeromonas schub...
WP_081837509  17 GGASAGELRPghaSNLCLDVKGGldq---snGTSIIVFPCNGGdNQSFTFMg--dGTIRAG----RRCVDISGgaar--- 84  Xanthobacter sp...
WP_083872615  38 PAQSRGEIRGq--GNRCIDVAGGevkdannnPSPLILFPCTGGkNQKWSFLs--nGTIRGQg---NRCIDVAGgevedsn 110 Calothrix sp. P...
OYU29216     212 PQWGSGQIRGk--DGLCLDMSGRve-----rGTEAIVFNCHGGnNQRFSWSn--rGELRVG----GMCLDVAEgnre--- 275 Burkholderiales...
WP_122102324  52 YRTLAGRLTS---AYGCLDIGMDsrvgetrrGRNVIAWPCHGRdNQQWSFDh---GLLRSRagrgNWCLDVDFnsrigtn 125 Lysobacter pyth...
Feature 1                                                                                        
1ISV_A       374 --gtKVQIYSCWGGdNQKWRLNsDGSIVGVq--sGLCLDAVGGgt----aNGTLIQLYSCSn----------GSNQRWTR 435 Streptomyces ol...
1V6W_A       374 --gtKVQIYSCWGGdNQKWRLNsDGSIVGVq--sGLCLDAVGGgt----aNGTLIQLYSCSn----------GSNQRWTR 435 Streptomyces ol...
ESQ80570      90 kngtPLVVTNCNSSpAQKWVNDeKGFLRNEe---GFCADVQFGsk----sDGARIIAYKCEeewalwskkaaKSNQRFGF 162 Asticcacaulis s...
WP_023454480 234 ---nTLEMAACNGSgEQDWTFTmEGLLRTRn---NLCGDILRFer----rPGTPVIAWECTa----------TDNQKWYP 293 Asticcacaulis s...
TAD82098      89 --gaPATVQPCTNAsTQRFGFQsNGTLRNEn---GLCLDIEGGar----gDGARILSYSCHg----------GTNQQWYP 149 Sphingomonadale...
ALP39433     118 -pgaRVIAWDCHGGsNQQWRWE-RGRLVSRn--sGLCLDVERGrs----eSGTPVLLWTCHg----------GDNQRFRW 179 Aeromonas schub...
WP_081837509  85 -agdRVIIYSCNGGaNQQWRVGaNGEIIGQn---NMCLDVPRFg-----gAGTGVVAWPCKsgg------edRSNQQWGT 149 Xanthobacter sp...
WP_083872615 111 gnssPLILFPCTGGnNQKWRFSsDGTIRGLg---DRCIDVAGGevedsngNHSPLILFPCTg----------GNNQKWRR 177 Calothrix sp. P...
OYU29216     276 -dgaRVIAWPCNGGnNQRWTRQ-GSEIRSRm--nGKCLDLKEGra----qPKQPVLLWRCNg----------GSNQRWSW 337 Burkholderiales...
WP_122102324 126 gagrNVIAWPCHGDeNQRWELF-GGQLINHtrgdKWCLDVALGapttlngPGRNVVAWRCNg----------GRNQKWRF 194 Lysobacter pyth...

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